Variant report

Variant	rs1838148
Chromosome Location	chr17:33819401-33819402
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:33819393-33819480	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SLFN12L	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11651218	1.00[ASN][1000 genomes]
rs11654381	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11657050	1.00[ASN][1000 genomes]
rs12949518	1.00[ASN][1000 genomes]
rs17548645	1.00[CHB][hapmap]
rs34658850	1.00[ASN][1000 genomes]
rs35077171	1.00[ASN][1000 genomes]
rs55990593	1.00[ASN][1000 genomes]
rs62078112	1.00[ASN][1000 genomes]
rs72825932	1.00[ASN][1000 genomes]
rs72825958	1.00[ASN][1000 genomes]
rs9898870	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055936	chr17:33327166-33884184	Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv543317	chr17:33327166-33884184	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv574741	chr17:33552275-33827134	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv978414	chr17:33817908-33822518	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1838148	SEZ6	cis	cerebellum	SCAN
rs1838148	RAB34	cis	cerebellum	SCAN
rs1838148	CPD	cis	cerebellum	SCAN
rs1838148	KIAA0100	cis	cerebellum	SCAN
rs1838148	KIAA0100	cis	parietal	SCAN
rs1838148	SLFN13	Cis_1M	lymphoblastoid	RTeQTL
rs1838148	RDM1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33812800-33820400	Strong transcription	Dnd41	blood
2	chr17:33815000-33820000	Weak transcription	Gastric	stomach
3	chr17:33815800-33826000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:33816000-33826400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr17:33816200-33820000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr17:33816400-33820600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr17:33816400-33821600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr17:33816600-33819800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr17:33816800-33820000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr17:33817000-33819600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr17:33817600-33820000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr17:33818000-33819800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr17:33818400-33820000	Weak transcription	GM12878-XiMat	blood
14	chr17:33818600-33819600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr17:33819200-33819600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr17:33819200-33819600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
17	chr17:33819400-33819600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
18	chr17:33819400-33819600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr17:33819400-33819800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr17:33819400-33820400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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